Just to give you all an update on this, after a bit of back and forth between Specialized and the LBS they are replacing the brakes with new Shimano kit which should provide greater clearance.

I still think that there is probably something wrong with the frame as otherwise I'm sure there would have been some recall unless the instructed the LBS's to change these Spec'd "23/25" Roubiax Pro tires with 23's.